Weed flora is considered harmful for crop growth and yield, but it is fundamental for preserving biodiversity in agroecosystems. Two three-year trials were conducted in Italy (two different sites) to assess the effect of six herbicide treatments on the weed flora structure of an oilseed rape crop. We applied metazachlor during the pre-emergence stage at 25%, 50%, 75%, and 100% of the labelled dose (M25, M50, M75, M100); trifluralin (during the first growing season); post-emergence treatment (PE); and a weedy control (W). Species richness, and diversity indices were used to characterize weed flora composition and to evaluate the effect of herbicide treatments on the considered variables. Results highlighted that the weed community is characterized by a higher diversity in underdosed than in M100 treated plots. Raphanus raphanistrum and Sinapis arvensis were the most common species in M75 and M100 treatments in both sites, while more weed species were detected in underdosed treatments and in weedy plots. The highest Shannon index values were observed in the underdosed treatments. In general, only a slightly similar trend was observed between sites, weed abundance and diversity being positively affected both by low-input herbicide management and by environmental factors (e.g., pedoclimatic situation and previous crop).